/*
 * smithWaterman.h
 *
 *  Created on: 17-10-2011
 *      Author: pawel
 */

#ifndef SMITHWATERMAN_H_
#define SMITHWATERMAN_H_

#include"optAlgV.h"
struct cell;
struct optAlgParam;
/**
 * This class implements Needleman - Wunsch Algorithm
 */
class smithWaterman: public optAlgClass{
public:
	/*
		 * This metod starts algorithm
		 * @return list of best alignments
		 *
		 */
	std::list<cell> run(const optAlgParam&);
	~smithWaterman();
};



#endif /* SMITHWATERMAN_H_ */
